version 1.1

cran · Jan 17, 2024 · 2a00ec3 · 2a00ec3
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,25 +1,56 @@
 Package: approxOT
 Type: Package
 Title: Approximate and Exact Optimal Transport Methods
-Version: 1.0.2
-Date: 2022-03-16
+Version: 1.1
+Date: 2024-01-15
 Authors@R: 
-    person("Eric", "Dunipace", 
+    c(person("Eric", "Dunipace", 
         role = c("aut", "cre"),
         email = "edunipace@mail.harvard.edu",
-        comment = c(ORCID = "0000-0001-8909-213X"))
-Author: Eric Dunipace [aut, cre] (<https://orcid.org/0000-0001-8909-213X>)
+        comment = c(ORCID = "0000-0001-8909-213X")),
+    person(given = "Espen",
+        family = "Bernton",
+        role = c("ctb"),
+        comment = "'Hilbert Sort' adapted from their code"),
+    person(given = "Mathieu",
+        family = "Gerber",
+        role = c("ctb"),
+        comment = "'Hilbert Sort' adapted from their code"),
+    person(given = "Pierre",
+        family = "Jacob",
+        role = c("ctb"),
+        comment = "'Hilbert Sort' adapted from their code"),
+    person(given = "Dominic", 
+        family = "Schuhmacher", 
+        email = "dominic.schuhmacher@mathematik.uni-goettingen.de", 
+        role = c("ctb"),
+        comment = "'Shortsimplex' optimal transport method adapted from their code"),
+    person(given = "Nicolas", 
+        family = "Bonneel", 
+        role = "ctb", 
+        comment = "'network simplex' algorithm adapted from their code")
+        )
 Maintainer: Eric Dunipace <edunipace@mail.harvard.edu>
 Description: R and C++ functions to perform exact and 
-  approximate optimal transport. All C++ methods are linkable 
+  approximate optimal transport. All C++ methods can be linked 
   to other R packages via their header files. 
-License: GPL (>= 3.0)
+License: GPL (== 3.0)
 Imports: Rcpp (>= 1.0.3), stats
 LinkingTo: Rcpp, RcppEigen, RcppCGAL, BH
 BugReports: https://github.com/ericdunipace/approxOT/issues
 Suggests: testthat (>= 2.1.0), transport
-RoxygenNote: 7.1.1
+Encoding: UTF-8
+RoxygenNote: 7.2.3
+URL: https://github.com/ericdunipace/approxOT
 NeedsCompilation: yes
-Packaged: 2022-03-17 02:43:34 UTC; eifer
+Packaged: 2024-01-16 06:40:21 UTC; eifer
+Author: Eric Dunipace [aut, cre] (<https://orcid.org/0000-0001-8909-213X>),
+  Espen Bernton [ctb] ('Hilbert Sort' adapted from their code),
+  Mathieu Gerber [ctb] ('Hilbert Sort' adapted from their code),
+  Pierre Jacob [ctb] ('Hilbert Sort' adapted from their code),
+  Dominic Schuhmacher [ctb] ('Shortsimplex' optimal transport method
+    adapted from their code),
+  Nicolas Bonneel [ctb] ('network simplex' algorithm adapted from their
+    code)
 Repository: CRAN
-Date/Publication: 2022-03-17 11:40:12 UTC
+Date/Publication: 2024-01-16 11:50:02 UTC
diff --git a/MD5 b/MD5
@@ -1,17 +1,17 @@
-17dd4988b1c0c0176885aa3113f1ab4f *DESCRIPTION
-9fbdc692ea6fbaca50a7af68505b86fa *NAMESPACE
-6f99890dc04a2890d5e681cf2c38bebc *R/RcppExports.R
-38f63ac108c704c098adb38f4dc1bf1c *R/approxOT-package.R
+97191d086628e918c2de61c40f9652d5 *DESCRIPTION
+12e7897acc7ea6d9ed0ecb167edcb3d0 *NAMESPACE
+7eea561ad2d6968f615110f5eeb0fb1b *NEWS.md
+a631a11dd152daa2ae50f5e14ecb73f0 *R/RcppExports.R
+06b0d69c8982094376f62f1f0d4107aa *R/approxOT-package.R
 e89a14923f71ebdcf13fe33720903d14 *R/cost_calculation.R
 f6e038fc2a5c9d9c92ed343875268bfd *R/hilbert.projection.R
-b4c05a951e57184a971f2acc6440c3f9 *R/sinkhorn.R
-ad36cef7a9aecde7345b10a8fd3869cf *R/transport_options.R
-36958fd303db2cb31128755e69856c3e *R/transport_plan.R
-311b0d3ad8f09ecc724c1592b5100036 *R/unload.R
-7f8b1cde45986aa4fe02f40495ce2d9a *R/wasserstein_distance.R
-480ed25f463cf153da446d369cc30030 *README.md
-4c468a3dda16ec70573948ba2307bcf4 *inst/CITATION
-212874d8f2d98598293a57753726e73f *inst/include/approxOT_types.h
+92c7ebfc0dbdcfcf44f334f1f4fb7960 *R/sinkhorn.R
+fc3c58383a1360195ef5832a20c3bf62 *R/transport_options.R
+ea0a55e237bcb86b4405df9b0bd2b075 *R/transport_plan.R
+a8ad5414518cf2c47a2979e47a59a8e1 *R/wasserstein_distance.R
+fa52ca3b61c3ad65d450f62c73cf2e5e *README.md
+2e98e4b4ccf8580887430f6745c58223 *inst/CITATION
+96298fbfc62f47b51228b0a49b2b434f *inst/include/approxOT_types.h
 eb436d6657691aa863a72656186276b0 *inst/include/cost.h
 4597916ea7a841fd78a11dfaec20db9b *inst/include/full_bipartitegraph.h
 0d603a0b2f7eaba69ef299c2b20bd8f3 *inst/include/hilbert_cgal.h
@@ -28,55 +28,61 @@ e23e89153b9ecf7dd49d2b55f4e12422 *inst/include/trans_gandkhorn.h
 2b2395e6f5ad3a08b417bd9f31f70b00 *inst/include/trans_randkhorn.h
 c64aea71a0f6f6f4f0bcae065484fd5c *inst/include/trans_rank.h
 ad10d58988825a440cee1feb6dc5ef69 *inst/include/trans_shortsimplex.h
-bef5c93b23d7d2ead6ecd3f60014002b *inst/include/trans_sinkhorn.h
+44269637b1f1dbd3c24fd477bd80749f *inst/include/trans_sinkhorn.h
 a280ae57738632ce2dbe4865d88fc912 *inst/include/trans_swap.h
 c74777fa68b59bcd78c5c551dd07c210 *inst/include/trans_univariate.h
 90d10ef4657954b575ee7e7cc58aa3b1 *inst/include/trans_univariate_approx_pwr.h
 059decd76013ef6b6c0bdda77713c035 *inst/include/transport.h
 dabbf34aee9a5abae8ea3c997faded2e *inst/include/utils.h
 a02025eeb3bba22eef8e3e9872d654e1 *inst/include/wasserstein.h
-02c0fde86acfe291d7741cc91dc0bc4d *man/approxOT-package.Rd
+b3c5e1e00a4db197d6a274bd92d67401 *man/approxOT-package.Rd
+67e4a47a79f15f8cae3e97848dae7bba *man/as.matrix.transport.plan.Rd
+ffa5208ece87198e95c780de36f89fdf *man/as.transport.plan.Rd
 7e600afb27119941489f7728ea749f27 *man/cost_calc.Rd
+1cc9fca3f58a5d34057f445cee64f97b *man/dist_2d_to_1d.Rd
 cc30319d1ac5ceeae61d670ac895f4e2 *man/general_1d_transport.Rd
 da8c8bcb69470af52e7a5b2fc25570e7 *man/hilbert.projection.Rd
 80a97f51ec324464ed2976f8489bbab8 *man/hilbert_proj_.Rd
+7f0576c37be8e66666726f0bfdde01db *man/is.transport.plan.Rd
+f38af1feaf1d94330643e1baf60426c3 *man/round_transport_matrix.Rd
 41208402d74440e69edad0112d6d376b *man/sinkhorn_distance.Rd
-3dc9063765331f08febb48cd1ee51472 *man/sinkhorn_pot.Rd
+bea865ba22e12bde0219b869e7237b29 *man/sinkhorn_pot.Rd
 e9d43312b66ed6b7906d33b7d382338c *man/sinkhorn_transport.Rd
-c249f2f549f9c49860c8824539a298ad *man/transport_options.Rd
-9989e719a3f4bf5b9782c95b1f9cc6ac *man/transport_plan.Rd
-ef90bdbb031a55d8864f447e227a00a1 *man/transport_plan_given_C.Rd
+e73ad6f4b2bd99c763cf8bf4d0187575 *man/transport_options.Rd
+8302fe391459ff8118c91d37fa71d24c *man/transport_plan.Rd
+fdb116056216b216ff4bc85b67f58580 *man/transport_plan_given_C.Rd
 452ecf171a57c89063c2cd32434dc458 *man/transport_plan_multimarg.Rd
-a6f646d3ecd74f526caa073b0dff2d4b *man/wasserstein.Rd
+e71d734798a150ce32a82ddb11cd08bf *man/wasserstein.Rd
 36808b5a1ae1985d1b39c7082ea3787e *src/Makevars
 f85e1e7a2701c8a8158d5cbd7e0338e5 *src/Makevars.win
-7b60fb130fd2b35435a96bc34c3e82eb *src/RcppExports.cpp
+e92fa1b866ab0174456188f39d88ad42 *src/RcppExports.cpp
 49021e38b3c7bbdf5b8054f6abdf2ffb *src/cost.cpp
 babb4706ef54cd811d58a0e2eacb2d0c *src/hilbert_cgal.cpp
 6f2638b646746faf1cb8570d24e46d41 *src/hilbert_projection.cpp
 8284b7b9df1c0e15dc9c8e277b08340c *src/networkflow.cpp
-f943a99f31dbe84692c121a3484a4698 *src/round_feasible.cpp
+ba6543970298f2f272042744d7bf387d *src/round_feasible.cpp
 f02a6d33280c2b3a0f959b270f5af6d5 *src/shortsimplex.c
 41ba408ab047211fb91406d088f74d4f *src/sinkhorn_test.cpp
 68beead4ce2a14a7fa754492c54a0c64 *src/sort.cpp
 e12e3fcddfa14e85518c851484a3e3d2 *src/systematic_sample.cpp
-cdd858e511fbb7fbb41f768dabc5cd01 *src/trans_approxOT.cpp
+5b8c8ca21d77540bd2127bace3ff3b84 *src/trans_approxOT.cpp
 ea5a7d5665da9ae50a50e494202751b2 *src/trans_gandkhorn.cpp
 5cdbd68a93789760913dfd3c456d10df *src/trans_greenkhorn.cpp
 87c99b4b0090269538cb4c3a5b7fa75a *src/trans_hilbert.cpp
 b679a0824ac45bdc49bf90daed8c8510 *src/trans_randkhorn.cpp
 73f6aba1bedf54bb50ad57adb4b8e3fa *src/trans_rank.cpp
 81f0800b9c07c573abb41d012c32ca5c *src/trans_shortsimplex.cpp
-061884405b51201b1bf60726b902d35b *src/trans_sinkhorn.cpp
+277bd700efb6ce296c39d0e16a6a6916 *src/trans_sinkhorn.cpp
 1d47e723a68bdaa7c8fbf2a4dde1b420 *src/trans_swap.cpp
 e4758bc972ae748200814c028b551124 *src/trans_univariate.cpp
 b4474ba7a38371a72a188fee5b0727c9 *src/trans_univariate_approx_pwr.cpp
-3d404f4b5a8eadb3b4869e4ca30de75e *src/transport.cpp
-6ea5b2133bab675b93b3b6477af507da *src/utils.cpp
+a4f0cdd5035573edf41c6ded86e8714e *src/transport.cpp
+0d668fd53c7cb943ab024aeb8e73a923 *src/utils.cpp
 6473d081693854b3ed38e877e1015295 *src/wasserstein.cpp
 f42704eb6cd1acfd149d06a89c47640e *tests/testthat.R
 1a4516e061efac67730d2a9634504c05 *tests/testthat/test-general_hilbert_transport.R
 644760a1befa1c0fefd491c368ba6763 *tests/testthat/test-hilbert.R
-dd67d96328b4b3142862ee72a117d2c3 *tests/testthat/test-transport_plan.R
+96a47a50effd36dd405ba2c3f87add5c *tests/testthat/test-sinkhorn_pot_.R
+d3b304772762841d77d6fca0141bea03 *tests/testthat/test-transport_plan.R
 d5ad857c16b7aae050f35c514ffe61ec *tests/testthat/test-transport_plan_multimarg.R
-452cccd2ab98505eb0e18c433ccf5ff8 *tests/testthat/test-wasserstein.R
+00171adaf7f46d2c23dd87e7f080e8a5 *tests/testthat/test-wasserstein.R
diff --git a/NAMESPACE b/NAMESPACE
@@ -1,8 +1,11 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method(base::as.matrix,transport.plan)
+export(as.transport.plan)
 export(cost_calc)
 export(general_1d_transport)
 export(hilbert.projection)
+export(is.transport.plan)
 export(sinkhorn_pot)
 export(transport_options)
 export(transport_plan)
@@ -11,4 +14,4 @@ export(transport_plan_multimarg)
 export(wasserstein)
 importFrom(Rcpp,evalCpp)
 importFrom(Rcpp,sourceCpp)
-useDynLib(approxOT)
+useDynLib(approxOT, .registration = TRUE)
diff --git a/NEWS.md b/NEWS.md
@@ -0,0 +1,11 @@
+# approxOT
+
+## Version 1.1
+
+* Added a `NEWS.md` file to track changes to the package.
+* Added a `as.matrix` function to convert transportation plans to matrices.
+* Added a `as.transport.plan` to convert from transportation matrix to transportation plan.
+* Added classes to support these two functions.
+* Added support for log domain calculations for the sinkhorn method. This can be accessed with "sinkhorn_log" as the method.
+* Fixed typo in C files incorrectly referencing Rcpp::stop
+* updated DLL registrations in Namespace
diff --git a/R/RcppExports.R b/R/RcppExports.R
@@ -2,15 +2,15 @@
 # Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
 
 cost_calculation_ <- function(A_, B_, p) {
-    .Call('_approxOT_cost_calculation_', PACKAGE = 'approxOT', A_, B_, p)
+    .Call(`_approxOT_cost_calculation_`, A_, B_, p)
 }
 
 multi_marg_final_cost_ <- function(idx_, data_, mass_, M, D, p, ground_p) {
-    .Call('_approxOT_multi_marg_final_cost_', PACKAGE = 'approxOT', idx_, data_, mass_, M, D, p, ground_p)
+    .Call(`_approxOT_multi_marg_final_cost_`, idx_, data_, mass_, M, D, p, ground_p)
 }
 
 multi_marg_given_dist_ <- function(idx_, mass_, cost_, M, N_cost, p) {
-    .Call('_approxOT_multi_marg_given_dist_', PACKAGE = 'approxOT', idx_, mass_, cost_, M, N_cost, p)
+    .Call(`_approxOT_multi_marg_given_dist_`, idx_, mass_, cost_, M, N_cost, p)
 }
 
 #' Returns orders along the Hilbert space-filling Curve
@@ -19,38 +19,74 @@ multi_marg_given_dist_ <- function(idx_, mass_, cost_, M, N_cost, p) {
 #' @return An integer vector of orders
 #' @keywords internal
 hilbert_proj_ <- function(A) {
-    .Call('_approxOT_hilbert_proj_', PACKAGE = 'approxOT', A)
+    .Call(`_approxOT_hilbert_proj_`, A)
+}
+
+round_2_feasible_ <- function(F, mass_a, mass_b) {
+    .Call(`_approxOT_round_2_feasible_`, F, mass_a, mass_b)
 }
 
 sinkhorn_ <- function(p_, q_, cost_matrix_, epsilon, niterations) {
-    .Call('_approxOT_sinkhorn_', PACKAGE = 'approxOT', p_, q_, cost_matrix_, epsilon, niterations)
+    .Call(`_approxOT_sinkhorn_`, p_, q_, cost_matrix_, epsilon, niterations)
+}
+
+generate_S <- function(cost, f, g, eta) {
+    .Call(`_approxOT_generate_S`, cost, f, g, eta)
+}
+
+rowLogSumExp <- function(Mat) {
+    .Call(`_approxOT_rowLogSumExp`, Mat)
+}
+
+colLogSumExp <- function(Mat) {
+    .Call(`_approxOT_colLogSumExp`, Mat)
+}
+
+rowMin_eps <- function(cost, f, g, eta) {
+    .Call(`_approxOT_rowMin_eps`, cost, f, g, eta)
+}
+
+colMin_eps <- function(cost, f, g, eta) {
+    .Call(`_approxOT_colMin_eps`, cost, f, g, eta)
+}
+
+rowMin_eps_KL <- function(cost, f, g, eta, log_a, log_b) {
+    .Call(`_approxOT_rowMin_eps_KL`, cost, f, g, eta, log_a, log_b)
+}
+
+colMin_eps_KL <- function(cost, f, g, eta, log_a, log_b) {
+    .Call(`_approxOT_colMin_eps_KL`, cost, f, g, eta, log_a, log_b)
 }
 
 sinkhorn_pot_ <- function(mass_a, mass_b, cost_matrix, epsilon, niterations, unbiased, cost_matrix_A, cost_matrix_B) {
-    .Call('_approxOT_sinkhorn_pot_', PACKAGE = 'approxOT', mass_a, mass_b, cost_matrix, epsilon, niterations, unbiased, cost_matrix_A, cost_matrix_B)
+    .Call(`_approxOT_sinkhorn_pot_`, mass_a, mass_b, cost_matrix, epsilon, niterations, unbiased, cost_matrix_A, cost_matrix_B)
+}
+
+sinkhorn_pot_log_ <- function(mass_a, mass_b, cost_matrix, epsilon, niterations, unbiased, cost_matrix_A, cost_matrix_B) {
+    .Call(`_approxOT_sinkhorn_pot_log_`, mass_a, mass_b, cost_matrix, epsilon, niterations, unbiased, cost_matrix_A, cost_matrix_B)
 }
 
 transport_C_ <- function(mass_a_, mass_b_, cost_matrix_, method_, epsilon_, niter_, unbiased_, threads_, cost_matrix_A_, cost_matrix_B_) {
-    .Call('_approxOT_transport_C_', PACKAGE = 'approxOT', mass_a_, mass_b_, cost_matrix_, method_, epsilon_, niter_, unbiased_, threads_, cost_matrix_A_, cost_matrix_B_)
+    .Call(`_approxOT_transport_C_`, mass_a_, mass_b_, cost_matrix_, method_, epsilon_, niter_, unbiased_, threads_, cost_matrix_A_, cost_matrix_B_)
 }
 
 transport_ <- function(A_, B_, p, ground_p, method_, a_sort, epsilon_ = 0.0, niter_ = 0L, unbiased_ = FALSE, threads_ = 1L) {
-    .Call('_approxOT_transport_', PACKAGE = 'approxOT', A_, B_, p, ground_p, method_, a_sort, epsilon_, niter_, unbiased_, threads_)
+    .Call(`_approxOT_transport_`, A_, B_, p, ground_p, method_, a_sort, epsilon_, niter_, unbiased_, threads_)
 }
 
 transport_swap_ <- function(A_, B_, idx_, mass_, p, ground_p, tolerance_, niter_ = 0L) {
-    .Call('_approxOT_transport_swap_', PACKAGE = 'approxOT', A_, B_, idx_, mass_, p, ground_p, tolerance_, niter_)
+    .Call(`_approxOT_transport_swap_`, A_, B_, idx_, mass_, p, ground_p, tolerance_, niter_)
 }
 
 wasserstein_ <- function(mass_, cost_, p, from_, to_) {
-    .Call('_approxOT_wasserstein_', PACKAGE = 'approxOT', mass_, cost_, p, from_, to_)
+    .Call(`_approxOT_wasserstein_`, mass_, cost_, p, from_, to_)
 }
 
 wasserstein_p_iid_ <- function(X_, Y_, p) {
-    .Call('_approxOT_wasserstein_p_iid_', PACKAGE = 'approxOT', X_, Y_, p)
+    .Call(`_approxOT_wasserstein_p_iid_`, X_, Y_, p)
 }
 
 wasserstein_p_iid_p_ <- function(X_, Y_, p) {
-    .Call('_approxOT_wasserstein_p_iid_p_', PACKAGE = 'approxOT', X_, Y_, p)
+    .Call(`_approxOT_wasserstein_p_iid_p_`, X_, Y_, p)
 }
 
diff --git a/R/approxOT-package.R b/R/approxOT-package.R
@@ -4,7 +4,7 @@
 #' @author Eric Dunipace
 #' @docType package
 #' @name approxOT
-#' @useDynLib approxOT
+#' @useDynLib approxOT, .registration = TRUE
 #' @importFrom Rcpp sourceCpp 
 #' @importFrom Rcpp evalCpp
 #' @rdname approxOT-package